Protocols and Recipes

Below are protocols and recipes used in Blattner lab.

Microarray

*E. coli Total RNA Labeling for High Density Oligonucleotide Array [PDF]
Labeling E. coli total RNA for high density oligonuceotide array like Affymetrix E. coli antisense genome array. [updated/corrected 05/30/2007]

*E. coli Total RNA Isolation [PDF]
Stablize E. coli RNA with Qiagen Bacteria RNA Protect Reagent and isolate total RNA with Epicentre MasterPure RNA Purification Kit. [updated 07/31/2003]

*E. coli Total RNA Labeling for Spotted Microarray [PDF]
Label E. coli Total RNA with CyDye-dUTP directly using Invitrogen Superscript II reverse transcriptase. [updated/corrected 05/30/2007]

* E. coli Genomic DNA Labeling [PDF]
Label fragmented E. coli genomic DNA with CyDye-dUTP directly using Klenow Fragment. [updated 02/10/2002]

* Spotted array Hybridization [PDF]
Hybridize CyDye-dUTP labeled probes to E. coli microarray printed on poly-lysine coated slide (provided by GEC) using Sigma ArrayHyb Buffer. [updated 02/10/2002]

Mutagenesis

* Tn5 Mutagenesis [PDF]
Mutate E. coli K-12 genes with Tn5 Transposon. [updated 05/11/2002]

Media

These are our protocols for preparing Neidhardt's MOPS-based defined media. These media are used for the global transcription analyses, and are now available commercially from TekNova Inc.
* EZ Rich Defined Medium [PDF]
* MOPS Minimal Medium [PDF]

 


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